San Francisco is at 90 murders now, or 89, according to the SF Chronicle, up from 85 for all of 2006, according to the SFPD (or 86, according to the FBI). It should be safe to say that 2005's 10-year record of 96 will be broken by the end of the year. It's certainly possible that the next highest record, 103 murders in 1995 (according to Chronicle. FBI says 99), may also be broken, which would give SF the highest murder rate since 1993, when 133 people were killed, according to the Chronicle (FBI says 129 killed). That record will probably not be broken unless there's some insane surge in killings.
The discrepancy between my count and the Chronicle's may be Hugues De La Plaza, who's death isn't officially counted as a murder so far, as the Medical Examiner has not released any official ruling on the cause of his death. Thanks to G.W. Schulz of the SFBG for the information on this, which he posted in a comment here.
Also, for those who had been wondering about the body in front of the Hilton last month, it was not a shooting. The victim either fell, was pushed, or jumped off of a balcony on the Hilton. Details are here.
Lastly, I'm pretty sure that the man I had reported as being shot and run over, in the suspicious/unverified deaths section, was actually the robber who was shot and run over by a father-son vigilante duo (he survived).